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- PDB-6kh2: Crystal structure of Nicotinic acid mononucleotide adenylyltransf... -

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Basic information

Entry
Database: PDB / ID: 6kh2
TitleCrystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132L/W176Y from Escherichia coli
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsLYASE / Crystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132L/W176Y from Escherichia coli
Function / homology
Function and homology information


NAD+ biosynthetic process via the salvage pathway / 'de novo' NAD+ biosynthetic process from L-aspartate / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD+ biosynthetic process / ATP binding
Similarity search - Function
Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable nicotinate-nucleotide adenylyltransferase / Nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli NCCP15648 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsFeng, Y. / Xue, S. / Zhao, Z. / Wang, X.
CitationJournal: To Be Published
Title: Crystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132L/W176Y from Escherichia coli
Authors: Xue, S. / Zhao, Z. / Wang, X. / Feng, Y.
History
DepositionJul 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable nicotinate-nucleotide adenylyltransferase
B: Probable nicotinate-nucleotide adenylyltransferase
C: Probable nicotinate-nucleotide adenylyltransferase
D: Probable nicotinate-nucleotide adenylyltransferase
E: Probable nicotinate-nucleotide adenylyltransferase
F: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)146,7656
Polymers146,7656
Non-polymers00
Water00
1
A: Probable nicotinate-nucleotide adenylyltransferase
D: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)48,9222
Polymers48,9222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable nicotinate-nucleotide adenylyltransferase
F: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)48,9222
Polymers48,9222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable nicotinate-nucleotide adenylyltransferase
E: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)48,9222
Polymers48,9222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.688, 130.209, 106.736
Angle α, β, γ (deg.)90.000, 103.505, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Probable nicotinate-nucleotide adenylyltransferase / Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide ...Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide adenylyltransferase / NaMN adenylyltransferase


Mass: 24460.787 Da / Num. of mol.: 6 / Mutation: P22K,Y84V,Y118D,C132L,W176Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli NCCP15648 (bacteria) / Gene: nadD, A610_610 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A222QGJ8, UniProt: P0A752*PLUS, nicotinate-nucleotide adenylyltransferase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 1.4M Sodium phosphate monobasic monohydrate-Potassium phosphate dibasic, pH 8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9798 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.04→50 Å / Num. obs: 27395 / % possible obs: 71.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 67.99 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.135 / Net I/σ(I): 4.85
Reflection shellResolution: 3.05→3.15 Å / Redundancy: 1.7 % / Rmerge(I) obs: 1.2 / Num. unique obs: 1736 / % possible all: 68.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4K

1k4k


Resolution: 3.04→48.7 Å / SU ML: 0.3964 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.7468
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2679 1359 4.96 %
Rwork0.2319 26024 -
obs0.2336 27383 63.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.77 Å2
Refinement stepCycle: LAST / Resolution: 3.04→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10189 0 0 0 10189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003310450
X-RAY DIFFRACTIONf_angle_d0.740114257
X-RAY DIFFRACTIONf_chiral_restr0.04371584
X-RAY DIFFRACTIONf_plane_restr0.00671884
X-RAY DIFFRACTIONf_dihedral_angle_d12.446382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.150.3803840.36381646X-RAY DIFFRACTION40.21
3.15-3.280.34321080.30692229X-RAY DIFFRACTION54.68
3.28-3.430.30981280.29532504X-RAY DIFFRACTION60.88
3.43-3.610.34341410.28112622X-RAY DIFFRACTION64.45
3.61-3.830.30221290.24692721X-RAY DIFFRACTION66.09
3.83-4.130.25211890.22162907X-RAY DIFFRACTION71.7
4.13-4.550.26981380.19332959X-RAY DIFFRACTION71.67
4.55-5.20.20841540.20562871X-RAY DIFFRACTION70.01
5.2-6.550.28241510.22722894X-RAY DIFFRACTION70.1
6.55-48.70.22461370.21012671X-RAY DIFFRACTION63.83

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